PAINT, elongator is not a histone acetyltransferase PTHR11135

[ValWood]

it is involved in tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation

please delete http://www.uniprot.org/uniprot/O14023

histone acetyltransferase activity and regulation of transcription from RNA polymerase II promoter

(can't check the family as QuickGO is broken)

[ValWood]

see https://github.com/geneontology/go-annotation/issues?q=is%3Aissue+elongator+is%3Aclosed

for some history.

[ValWood]

The current def of elongator Definition A heterohexameric protein complex that is involved in modification of wobble nucleosides in tRNA. The complex can associate physically with hyperphosphorylated RNA polymerase II; it contains two discrete heterotrimeric subcomplexes. Source: PMID:23165209, PMID:17018299, GOC:vw, PMID:15769872, GOC:bhm, PMID:11689709, PMID:18755837, GOC:jh, PMID:11435442, GOC:mah Comment Despite its name, this complex is no longer thought to be directly involved in transcriptional elongation (PMID:23165209).

see this paper and other recent ones https://www.ncbi.nlm.nih.gov/pubmed/23165209

[ValWood]

Extensive work in budding yeast and fission yeast strongly support that Elongator is primarily implicated in tRNA modifications in these two species, which underlies a new mechanism that fundamentally contributes to gene expression regulation.

(all the transcription phenotypes are suppressed by tRNA overexpression)

[ValWood]

histone acetyltransferase activity |   | IDA | SGD | 2007-01-08 |   | Wittschieben BO, et al. (1999)PMID:10445034

This annotation was removed from SGD back in 2006 by Maria when the tRNA modification info came to light as is not now considered to be physiologically relevant (all phenotypes are suppressed by over-expression of tRNA...there are lots of more recent papers)

@srengel could you get someone take a look ?

https://www.yeastgenome.org/locus/YPL086C#go

[ValWood]

I'm a bit confused because I don't see the SGD annotation in the UniprotKB entry, but http://www.uniprot.org/uniprot/O14023 I do see a GOC mapping.... Seems very strange...

[ValWood]

In quickGo its just IBA and IDA, maybe you already removed it?

[srengel]

if the annotation was removed in 2006, it must have been added back in 2007.

to make sure i understand, you are asking that we re-remove the histone acetyltransferase MF annot for ELP3?

[ValWood]

yes the consensus is that it isn't a histone acetyltransferase according to papers post 2005

"This domain is not involved in histone acetyltransferase activity, but it could have a role in 5carboxymethyluridine modification through an unprecedented chemistry performed on acetyl-CoA [according to PMID:25151136]. It seems that the function of the domains of Elp3 is not exactly known."

see also https://github.com/geneontology/go-annotation/issues/1805 and linked tickets.

[pgaudet]

@srengel @ValWood Is this a case where NOT should be used, to make sure we don't repeat the mistake again?

Thanks, Pascale

[pgaudet]

@ValWood are you saying that the UniProt summary is incorrect ? http://www.uniprot.org/uniprot/Q9H9T3

[ValWood]

are you saying that the UniProt summary is incorrect ?

yes it's very out of date...

[pgaudet]

One problem is that UniProt has a mapping of Elongator complex protein 3 to EC:2.3.1.48, Histone acetyltransferase (this corresponds to the IEAs)

Same problem with InterPro. I will create separate tickets for those.

[pgaudet]

Please remove histone acetyl transferase and regulation of transcription annotations to ELP3 orthologs.

We also need to request groups with primary EXP annotations to add 'NOT' annotations to avoid confusion in the future.

@srengel SGD ELP3 @RLovering Human ELP3

[ValWood]

corrected https://github.com/geneontology/go-annotation/issues?q=is%3Aissue+elongator+is%3Aclosed

specifically https://github.com/geneontology/go-annotation/issues/1805